Technical Abstract:
Microsatellite sequences, alternatively called simple sequence repeats (SSRs), were identified from end sequences of a BAC library constructed from G. hirsutum 'Maxxa'. Eight hundred sequences were selected that contained di, tri, or tetra nucleotide repeats and PCR primers were designed to flank the SSRs. Selected SSR markers, polymorphic between G. hirsutum and G. barbadense, are being assayed on 181 recombinant inbred lines (RIL) and a set of monosomic lines developed from the cross of G. hirsutum TM-1 x G. barbadense 3-79 for assignment of the markers to cotton chromosomes and linkage groups. The RIL population is also being assayed for mapped, publicly available SSR markers to enable the eventual integration of our new markers into the cotton genetic map. Data on fiber quality for an original F2 of TM-1 x 3-79 will be used to identify putative QTLs linked to the SSR markers. The appeal of our BAC-end derived SSR markers is that the molecular marker cotton map may enable alignment of the original full length cotton sequences and help develop the cotton genome framework more fully. The average size of the full BAC sequences is 140 kb and one outcome of this research is that actual genetic distances (bases) can be compared with recombinant distances (i.e. cM) for our linked markers. Also QTL associations with markers from known BAC sequences may make more feasible the sequencing of putative genes associated with important traits in cotton.